Direct Measurements of Isoprene Autoxidation: Pinpointing Atmospheric Oxidation in Tropical Forests

2-Methyl-1,3-butadiene (isoprene), released from biogenic sources, accounts for approximately a third of hydrocarbon emissions and is mainly removed by hydroxyl radicals, OH, the primary initiator of atmospheric oxidation. In situ measurements in clean tropical forests (high isoprene and low NOx) have measured OH concentrations up to an order of magnitude higher than model predictions, which impacts our understanding of global oxidation. In this study, direct, laser flash photolysis, laser-induced fluorescence measurements at elevated temperatures have observed OH recycling in the presence of isoprene and oxygen under conditions where interference from secondary or heterogeneous chemistry is minimal. Our results provide the first direct, time-resolved, experimental validation of the theory-based Leuven Isoprene Mechanism (LIM1), based on isomerization of isoprene-RO2 radicals and OH regeneration, that partially accounts for model:measurement divergence in OH. While our data can be fit with only minor alterations in important LIM1 parameters, and the overall rate of product formation is similar to LIM1, there are differences with the recent experimental study by Teng et al. J. Am. Chem. Soc.2017, 139, 5367–5377. In addition, our study indicates that the dihydroperoxide products are significantly enhanced over previous estimates. Dihydroperoxides are chemical and photochemical sources of OH, and the implications of enhanced hydroperoxide formation on the agreement between models and observations in tropical forests are examined.


Mechanism from LIM1 for Addition of OH to the non-substituted double bond.
Scheme SI1 shows the LIM1 mechanism 1 for addition of the OH to the non-methyl end of isoprene; the other OH addition is given in the main text, Figure 1. OO

Complete reaction mechanism used for MATLAB data fitting
All 32 rate coefficients of the LIM1 were described using a generic four-parameter format: This format is flexible enough to generate all the required rate coefficients, e.g. setting n i , Ea i or Q i (the specific tunneling contribution, which is discussed further in section 4) to zero reduces the equation to a simpler form. The LIM1 mechanism and its rate coefficients are explicitly described using the following schemes where we have used the LIM1 nomenclature, and for ease of reading, have separated OH addition at the substituted double bond (Figure 1, CASE I), OH additional the non-substituted double bond ( Figure SI1, CASE II) and experimental parameters : Table S1 -Reaction mechanism used to fit experimental data. Nomenclature follows that of the LIM1 mechanism, where adjusted parameters are colour highlighted.

Experimental Details
Experiments were carried out in two distinctly different apparatus, where the main difference is how the hydroxyl radical, OH, is measured. In the conventional, low-pressure apparatus, 3,4 the OH is directly detected in situ in the reaction zone defined by the overlap of the, photolysis laser and the probe laser, see Figure SI1. In the high pressure apparatus, 5 the photolysis laser creates OH along the length of the reactor, but the OH is not measured in situ. The OH is sampled at the end of the reactor by passing through a pinhole into a lowpressure cell, where it is detected by laser induced fluorescence, LIF, see Figure SI2. This technique is known as fluorescence assay by gas expansion, FAGE, and is well known in the field measurement community. 6 The main difference in the present apparatus is that the OH is detected within 1 cm of the pinhole, where the gas is jetting, i.e. undergoing relatively few collisions. We have demonstrated that in this configuration the OH is sampled in ~20 microseconds and the kinetics are essentially unperturbed, i.e. identical to the kinetics in the low-pressure in situ OH cell. 2,4,5 In the high-pressure apparatus, the reaction zone is typically the volume within 1 -2 mm from the pinhole as the experiment is complete is 10 milliseconds.
The reason for deploying these two types of apparatus is because large [O 2 ] have to be added to the system, see  Figure SI1. Schematic of low-pressure reactor: the laser beams cross in the centre of the heated, multi-axes cell and defines the reaction zone where the OH is formed and monitored in situ, via detecting the fluorescence at right angles to the laser beams. Figure SI2. Schematic of high-pressure reactor. 5 The photolysis laser illuminates the heated reactor (green), where the reaction zone is defined by the volume within ~1-2 mm of the pinhole. The OH is detected in the low-pressure cell, blue, within 1-2 cm of the pinhole where the probed gas is jetting.
Besides where the OH is measured, both experimental apparatus operate on similar principles. Known amounts of gases (H 2 O 2 , isoprene, O 2 and N 2 ) are flowed into the reactor using calibrated mass flow controllers, where the gases reach a pre-set temperature controlled by the heaters of the reactor. The reaction is initiated by a photolysis laser, which is either the 248 nm output from a KrF excimer laser (Lambda Physik, LPX200) or the 266 nm output from a Nd:YAG laser (Quantel, Q-smart 850). The photolysis laser dissociates hydrogen peroxide and is a clean instant OH source: The OH is probed (typically at ~308 nm) using a tuneable wavelength dye laser (Sirah, PrecisionScan) by laser induced fluorescence (LIF); the resulting resonant fluorescence is passed through an optical filter (308 ± 5 nm, Barr Associates) and is detected via a photomultiplier (Electron Tubes) situated at right-angles to the plane of the lasers.
Additionally, some measurements were made via off resonant LIF, probing at 282 nm to generate the vibrationally excited A state and again monitoring at ~308 nm. In either case, the OH signal is a relative measure of the OH concentration and its time profile is determined by scanning the delay between the firing of the photolysis and dye lasers using a delay generator (BNC 555). The OH trace is the resultant of typically 200 time points, averaging between 3 -12 at each point (see Figure 2 for example traces).
Further details on the low-pressure cell can be found in a number of publications 3, 4 All the low pressure experiments were carried out between 100 -200 Torr total pressure. The highpressure apparatus is a more recent development but it has been described in detail in two recent publications. 5,7 The reactor consists of 2.0 cm diameter stainless tube, lined with a quartz tube. There is a quartz window at one end to admit the photolysis light and the other end is open and is close to a pinhole. The majority of the gas, at ~2 atmospheres, is pumped away but a representative sample flows through the pinhole into the low pressure cell, which is pumped with a roots blower down to a pressure below 1 Torr. The gas emerging through the pinhole supersonically expands and a cold jet is established for 1 -2 cm; dependent on pressure drop. It is in this jet where the OH is detected by LIF. As noted above, the OH measured in this zone is wholly representative of the kinetics in the high pressure part of the The OH removal kinetics for S-R2 follow a simple signal exponential loss:

Master equation modelling a) Overall lack of pressure dependence and tunnelling
Although the experiments have been carried out at low and high pressure, it has been assumed in the data analysis that the kinetics of LIM1 are independent of total pressure.
This assumption has been tested by performing some master equation simulations of the 1-5 and 1-6 H shift reactions, R5 and R6, starting from OH-isoprene + O 2 using the MESMER 9 software package.
The loss of OH-isoprene from the system is made up of several rate coefficients: RO 2 formation, re-dissociation and reaction to products. All these individual rate coefficients are pressure dependent, but the overall rate of formation of products is complex (a mixture of the rate coefficients given by the eigenvalue of the system) and is pressure independent. This result is true over all temperatures (250 -600 K) and pressures (50 -10 6 Torr) relevant to the present study, see Table SI1. This eigenvalue is equal to a sum of the equilibrium amount of R that directly "well-skips" 10 to products plus the equilibrium amount of RO 2 that thermally reacts to products. The contribution from each of these terms varies between low and high pressure, but the sum is constant, and hence pressure independent. This effect arises because the RO 2 re-dissociation is much faster than reaction to products, so that the R and RO 2 is at equilibrium on the reaction timescale. This lack of pressure independence was essentially maintained when R5 and R6 were coupled.  Figure   SI3. While it is acknowledged that calculating tunnelling factors has significant uncertainty,

b) Simulations of the branching ratio between HPALD and diHPCARP
Reaction of Z,Z'-OH-allyl with O 2 , R7, branches to form either HPALD (7a) or diHPCARP (7b). Peeters et al. calculated the surface for this reaction but did not explore the kinetics.
We have recalculated these surfaces of Peeters et al. and then carried out master equation analysis with the MESMER code. 9 These reactions that lead to HPALD and diHPCARP are independent, so the calculated rate coefficients (and branching ratio) are not absolute. The aim of these calculations is to determine how the branching ratio changes with temperature in order to extrapolate our results at high temperature to 298 K; we only need to know the relative change in k 7a and k 7b with temperature.
Overall, both oxygen addition reactions are characterised by rate coefficients that decrease with increased temperature, but the diHPCARP reaction, R7b, exhibits a slightly stronger negative temperature dependence. Our calculated BF HPALD (T) is shown in Figure SI4, where our k 7a and k 7b have been scaled in order to yield the result of Crounse et al. 12  The average temperature of our experiments is 509 K, see Table SM1.Therefore BF HPALD will be approximately 0.3 greater at our temperatures compared to 298 K. In scenarios 5,9,13 15 and 17, the BF was explored by imposing S-E3, where it was either fixed or adjusted via a scaling factor, S-E3 × BF scaling .

Figure SI4
-Calculated temperature dependence of BF HPALD scaled to be equal to Crounse et al. 12 at 298 K assuming LIM1.
In general, our results confirm that BF is less than 0.40 and probably smaller when its temperature dependence is taking into account. Our experiments directly probe OH, so reaction R7b is measured. It is assumed that HPALD is the other channel of R7 and this channel does not decompose to OH.

Data analysis (MATLAB)
Data analysis was carried out globally, simultaneously fitting parameters to the 94 OH time dependent traces. 13 This approach is required as the OH trace data are described by many rate coefficients and one trace alone will not guarantee a consistent and reliable extraction of temperature-dependent information. Global analysis is a technique that takes advantage of the relationships that exist in the data to better describe and identify the parameters of the system.
LIM1 is a fundamental description of the system, where ab initio structure calculations were undertaken to map out the potential energy surface of the reaction (the mechanism) and reaction rate theory was employed to calculate the rate coefficients.
In our analysis, LIM1 is the starting mechanism in our data analysis seeing as its network of reactions have been verified via ab initio calculation, and its rate coefficient parameters calculated via reaction rate theory. The parameters (see colours in Table SI1)  traces with the aid of the MATLAB ODE suite. 15 Floatable parameters were adjusted following the Trust Region Reflective Algorithm. 16 The objective function was defined as the sum of squared residuals (   calculated from a comparison between experimental measurements and their corresponding numerical simulation. Each trace is appropriately weighted using the   from fitting it individually using a flexible function, a bi-exponential. This individual fit   represents the best fit, so that in the global analysis the best value for   divided by the number of traces, n traces , is 1.0. From Table 1 it can be seen that χ 2 /n traces is within ~20% of 1.0, and section 7 shows these fits. Weighting using the individual   is normalising each trace for signal (amplitude) and the noise within the trace. The adjusted parameters are given in the scenarios together with the best-fit parameters.
In the analysis, the R7 reactions involve O 2 and their rate coefficients were not calculated in LIM1. To explore the importance of the R7 rate coefficient, fits to data were carried (via scenario 6) with k R7 initially floated. This did not return a define parameter. In subsequent fits, k R7 was fixed with a range of values, 10 -21 -10 -10 cm 3 molecule -1 s -1 . The results are summarized in Figure SI5, where it can be seen that CHISQ reduces as k R7 increases, but once k 7 ≥ 10 -13 cm 3 molecule s -1   reaches its minimum. This means that k 7 is not defined, except that it requires a minimum value. In our analysis k 7 was set > 4×10 -14 cm 3 molecule -1 s -1 .

Figure SI5
The dependence of the value of the fit parameter,   vs k 7 .

SCENARIOS
The LIM1 mechanism (and Caltech) is explored by starting with the basic LIM1 mechanism and is explored over a range of scenarios, where the following parameters have been

SUMMARY OF SCENARIOS
With the exception of the Caltech mechanism, these many scenarios (1-14) all provide a near equal good fit to the data. With respect to the kinetics of the system, it does not matter too much which model is chosen as they all lead to similar species profiles for the formation of products: MVK/MAC and diHPCARP/HPALD. This point is demonstrated in Figure SI6, where it can be seen that k(bulk) at 298 K is essentially the same for all the LIM1 (scenario 1) and LIM1-Leeds models. The Caltech model produces a much smaller k(bulk) lifetime, but this scenario fit is significantly worse and hence inconsistent with our data. In Figure SI6 Novelli et al. 11 There is more uncertainty in the branching ratio for R7, BF, see Figure SI7. It is clearly less than 0.4 and based on the temperature dependence of BF, see Figure SI4, is more likely to be ≤0.25, and most likely to be lower. (via the correlation matrix from the scenario fit to the data). These MC simulations allowed the half-life to be determined, which is used to calculate k(bulk), see Figure 2. It also allows the statistics on k(bulk) to be determined. Figure SI8 shows the species profiles for all products from the MC simulation of scenario 14. This scenario has the most floated parameters, with greatest errors, and still generates species profile with less than 30% uncertainty. It is noted that multivariate distribution sampling leads to less uncertainty than if MC sampled according to just the errors in the parameters, i.e. the correlations in the parameters serve to better define the product distributions.